Asymptomatic SARS-CoV-2 infection: A systematic review and meta-analysis

Estimating the potential public health and economic impact of vaccination strategies with an adapted vaccine in Colombia using a combined Markov-decision tree model

BACKGROUND

Using adapted COVID-19 vaccines targeting current variants in circulation is necessary for addressing the dynamic evolution of the SARS-CoV-2 virus and protecting against emerging variants. This study evaluated the impact of various vaccination strategies with an adapted vaccine in Colombia.

RESEARCH DESIGN AND METHODS

Using a previously published combined Markov-decision tree model adapted for the Colombia context, this study estimated the outcomes of different vaccination strategies targeting various age and risk groups. The model used age-specific epidemiology, clinical, cost, and quality of life inputs derived from the published literature and national surveillance data. Scenario and sensitivity analyses were conducted to assess uncertainty.

RESULTS

Compared to no vaccination, the vaccination strategy targeting older adults aged ≥65 years and the high-risk population was estimated to prevent 306,460 symptomatic cases, 5,200 hospitalizations, 3,381 deaths, and 39,454 lost QALYs, translating to total direct and societal cost savings of USD 70,840,305 and USD 128,918,995, respectively. These gains were further increased by expanding vaccination to additional age groups. Results were most sensitive to parameters for the attack rate and duration of protection.

CONCLUSIONS

Implementing vaccination strategies targeting a broader age range with an adapted vaccine would result in considerable health and economic benefits in Colombia.

Why gender and sex matter in infectious disease modelling: A conceptual framework

The COVID-19 pandemic underscored the differential impact of infectious diseases across population groups, with gender and sex identified as important dimensions influencing transmission and health outcomes. Sex-related biological factors, such as differences in immune response and comorbidities, contribute to men's heightened severity risks, while gender norms and roles influence exposure patterns, adherence to prevention measures, and healthcare access, influencing women's higher reported infection rates in certain contexts. Despite widely observed gender/sex disparities, infectious disease models frequently overlook gender and sex as key dimensions, leading to gaps in understanding and potential blind spots in public health interventions. This paper develops a conceptual framework based on the Susceptible-Exposed-Infectious-Recovered/Deceased (SEIR/D) compartmental model to map pathways through which gender and sex may influence susceptibility, exposure, transmission, recovery, and mortality. Using a narrative review of modelling, epidemiological, and clinical studies, this framework identifies and characterises the main social and biological mechanisms on this matter-including gendered occupational exposure, differential adherence to preventive measures, and disparities in healthcare-seeking behaviour-alongside sex-based differences in immune response and disease severity. The framework also examines potential gender-related variations in epidemiological surveillance data, highlighting disparities in testing uptake and hospitalisation referrals that could influence model outputs. By synthesising these insights, this paper provides a theoretical foundation for integrating gender and sex into infectious disease models. It advocates for interdisciplinary collaboration between modellers, social scientists, and clinicians to advance gender- and sex-sensitive modelling approaches. Accounting for gender and sex can enhance predictive accuracy, inform intervention strategies, and promote health equity in pandemic response.

Testing-isolation interventions will likely be insufficient to contain future novel disease outbreaks

Rapid identification and isolation of infected individuals with diagnostic testing plays a critical role in combating invasions of novel human pathogens. Unfortunately, unprepared health agencies may struggle to meet the massive testing capacity demands imposed by an outbreaking novel pathogen, potentially resulting in a failure of epidemic containment as occurred with COVID-19. Despite the critical importance of understanding the likelihood of such an outcome, it remains unclear how the particular characteristics of a novel disease will impact the magnitude of resource constraints on controllability. Specifically, is the failure of testing-isolation unique to COVID-19, or is this a likely outcome across the spectrum of disease traits that may constitute future epidemics? Here, using a generalized mathematical model parameterized for seven different human diseases and variants, we show that testing-isolation strategies will typically fail to contain epidemic outbreaks at practicably achievable testing capacities. From this analysis, we identify three key disease characteristics that govern controllability under resource constraints; the basic reproduction number, mean latent period, and non-symptomatic transmission index. Interactions among these characteristics play prominent roles in both explaining controllability differences among diseases and enhancing the efficacy of testing-isolation in combination with transmission-reduction measures. This study provides broad guidelines for managing controllability expectations during future novel disease invasions, describing which classes of diseases are most amenable to testing-isolation strategies alone and which will necessitate additional transmission-reduction measures like social distancing.

SARS-CoV-2 dynamics in New York City during March 2020-August 2023

BACKGROUND

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widespread since 2020 and will likely continue to cause substantial recurring epidemics. However, understanding the underlying infection burden and dynamics, particularly since late 2021 when the Omicron variant emerged, is challenging. Here, we leverage extensive surveillance data available in New York City (NYC) and a comprehensive model-inference system to reconstruct SARS-CoV-2 dynamics therein through August 2023.

METHODS

We fit a metapopulation network SEIRSV (Susceptible-Exposed-Infectious-(re)Susceptible-Vaccination) model to age- and neighborhood-specific data of COVID-19 cases, emergency department visits, and deaths in NYC from the pandemic onset in March 2020 to August 2023. We further validate the model-inference estimates using independent SARS-CoV-2 wastewater viral load data.

RESULTS

The validated model-inference estimates indicate a very high infection burden-the number of infections (i.e., including undetected asymptomatic/mild infections) totaled twice the population size ( > 5 times documented case count) during the first 3.5 years. Estimated virus transmissibility increased around 3-fold, whereas estimated infection-fatality risk (IFR) decreased by >10-fold during this period. The detailed estimates also reveal highly complex variant dynamics and immune landscape, and higher infection risk during winter in NYC over the study period.

CONCLUSIONS

This study provides highly detailed epidemiological estimates and identifies key transmission dynamics and drivers of SARS-CoV-2 during its first 3.5 years of circulation in a large urban center (i.e., NYC). These transmission dynamics and drivers may be relevant to other populations and inform future planning to help mitigate the public health burden of SARS-CoV-2.

Rethinking the evidence on COVID-19 in Africa

The COVID-19 pandemic was predicted to cause substantial mortality in Africa. However, some countries in Africa had a striking absence of overwhelmed hospitals and low reported mortality. The marked contrast with the overwhelmed hospitals and high mortality seen in Europe and other high-income settings was regarded as puzzling and a paradox. In this Review, we reflect on possible explanations for the paradox with particular reference to observations made on the ground in Kenya. The evidence is inconsistent with reduced viral transmission or poor surveillance as primary explanations for the discrepancy. Population age structure is an important but incomplete explanation of the epidemiology. Due to the high prevalence of asymptomatic infection, low mortality, and evidence of reduced inflammatory responses, we hypothesise that some populations in Africa might have reduced susceptibility to symptomatic COVID-19. The reduced inflammatory responses might result from immunoregulation or cross-reactive, pre-pandemic cellular immunity, although the evidence is not definitive. Local data are essential to develop public health policies that align with the reality on the ground rather than external perceptions.

Respiratory morbidity before and during the COVID-19 pandemic from birth to 18 months in a Swedish birth cohort

BACKGROUND

Respiratory infections in early life are an identified risk factor for asthma. We hypothesized that infection-prevention measures during the coronavirus disease 2019 (COVID-19) pandemic influenced the risk of respiratory morbidity and aeroallergen sensitization in early childhood.

OBJECTIVE

We compared respiratory morbidity and aeroallergen sensitization in children born before and during the pandemic.

METHODS

We compared a COVID-19 category (exposed children; n = 1661) to a pre-COVID-19 category (nonexposed children; n = 1676) by using data from the prospective population-based NorthPop Birth Cohort study in Sweden. Data on respiratory morbidity and concomitant medication were retrieved from national registers. Prospectively collected data on respiratory morbidity using web-based questionnaires at 9 and 18 months of age were applied. At age 18 months, serum IgE levels to aeroallergens were determined (n = 1702).

RESULTS

The risk of developing any respiratory tract infection (adjusted odds ratio [aOR] = 0.33 [95% CI, 0.26-0.42]), bronchitis (aOR = 0.50 [95% CI, 0.27-0.95]) and croup (aOR = 0.59 [95% CI, 0.37-0.94]) were decreased in the COVID-19 category. The risk of wheeze in the first 9 months was lower in the COVID-19 category (aOR = 0.70 [95% CI, 0.55-0.89]). There were also fewer prescriptions of antibiotics in the COVID-19 category. The prevalence of aeroallergen sensitization was similar between categories.

CONCLUSION

Children born during the COVID-19 pandemic demonstrated significantly decreased risks of respiratory infections and prescribed antibiotics until 18 months of age compared to children born before the COVID-19 pandemic. Whether this will affect the risk of developing asthma in childhood is being followed.

Analysis insights to support the use of wastewater and environmental surveillance data for infectious diseases and pandemic preparedness

Wastewater-based epidemiology is the detection of pathogens from sewage systems and the interpretation of these data to improve public health. Its use has increased in scope since 2020, when it was demonstrated that SARS-CoV-2 RNA could be successfully extracted from the wastewater of affected populations. In this Perspective we provide an overview of recent advances in pathogen detection within wastewater, propose a framework for identifying the utility of wastewater sampling for pathogen detection and suggest areas where analytics require development. Ensuring that both data collection and analysis are tailored towards key questions at different stages of an epidemic will improve the inference made. For analyses to be useful we require methods to determine the absence of infection, early detection of infection, reliably estimate epidemic trajectories and prevalence, and detect novel variants without reliance on consensus sequences. This research area has included many innovations that have improved the interpretation of collected data and we are optimistic that innovation will continue in the future.

Potential biases in test-negative design studies of COVID-19 vaccine effectiveness arising from the inclusion of asymptomatic individuals

The test-negative design (TND) is a popular method for evaluating vaccine effectiveness (VE). A "classical" TND study includes symptomatic individuals tested for the disease targeted by the vaccine to estimate VE against symptomatic infection. However, recent applications of the TND have attempted to estimate VE against infection by including all tested individuals, regardless of their symptoms. In this article, we use directed acyclic graphs and simulations to investigate potential biases in TND studies of COVID-19 VE arising from the use of this "alternative" approach, particularly when applied during periods of widespread testing. We show that the inclusion of asymptomatic individuals can potentially lead to collider stratification bias, uncontrolled confounding by health and healthcare-seeking behaviors (HSBs), and differential outcome misclassification. While our focus is on the COVID-19 setting, the issues discussed here may also be relevant in the context of other infectious diseases. This may be particularly true in scenarios where there is either a high baseline prevalence of infection, a strong correlation between HSBs and vaccination, different testing practices for vaccinated and unvaccinated individuals, or settings where both the vaccine under study attenuates symptoms of infection and diagnostic accuracy is modified by the presence of symptoms.

A longitudinal study depicting persistence of COVID-19 antibodies after half a year using chemiluminescent microparticle immunoassay among healthcare workers and frontline workers in Mumbai, India's largest metropoli

Introduction

Antibodies play a role in herd immunity, and studies estimate that COVID-19 antibody protection lasts approximately 1 to 4 months following COVID-19 vaccination and 6 to 8 months following infection. As healthcare workers and frontline workers were highly exposed to the infection, it is necessary to know if they have developed immunity against COVID-19.

Aim

To estimate the seroprevalence of SARS-CoV-2 antibodies among health care workers and frontline workers in Mumbai qualitatively and quantitatively and observe the change in antibody levels after 6 months.

Material and Methods

This longitudinal study was conducted over 9 months in two phases among 1544 healthcare workers (HCWs) and 1555 frontline workers (FLWs) aged above 18 years in Mumbai, Maharashtra, India. Participants' blood samples were analyzed using the SARS-CoV-2 IgG-II Quant assay for the qualitative and quantitative determination of IgG antibodies to SARS-CoV-2. A follow-up was done after 6 months.

Results

A total of 2733 (88.2%) of the 3099 participants were followed up in Phase II, which included 1370 (50.1%) FLWs and 1363 (49.9%) HCWs. The study found a seropositivity rate of 99.9% with a significantly higher antibody titre in BEST (public transport) workers, those vaccinated with precautionary doses, those vaccinated with precautionary doses with a history of confirmed COVID-19 disease, and participants over 45 years.

Conclusions

The study findings indicate a widespread seroconversion against COVID-19 and a beneficial effect of precautionary dose in addition to two doses of the COVID-19 vaccine. The role of subclinical infection needs to be explored.

Metapopulations, the Inflationary Effect, and Consequences for Public Health

AbstractThe metapopulation concept offers significant explanatory power in ecology and evolutionary biology. Metapopulations, a set of spatially distributed populations linked by dispersal, and their community and ecosystem level analogs, metacommunity and meta-ecosystem models, tend to be more stable regionally than locally. This fact is largely attributable to the interplay of spatiotemporal heterogeneity and dispersal (the inflationary effect). We highlight this underappreciated (but essential) role of spatiotemporal heterogeneity in metapopulation biology, present a novel expression for quantifying and defining the inflationary effect, and provide a mechanistic interpretation of how it arises and impacts population growth and abundance. We illustrate the effect with examples from infectious disease dynamics, including the hypothesis that policy decisions made during the COVID-19 pandemic generated spatiotemporal heterogeneity that enhanced the spread of disease. We finish by noting how spatiotemporal heterogeneity generates emergent population processes at large scales across many topics in the history of ecology, as diverse as natural enemy-victim dynamics, species coexistence, and conservation biology. Embracing the complexity of spatiotemporal heterogeneity is vital for future research on the persistence of populations.

The role of masks and respirators in preventing respiratory infections in healthcare and community settings

The covid-19 pandemic saw frequent changes and conflicts in mask policies and politicization of masks. On reviewing the evidence, including studies published after the pandemic, the data suggest respirators are more effective than masks in healthcare, but must be continuously worn to be protective. Healthcare and aged care settings amplify outbreaks, so protection of patients and staff is paramount. Most guidelines assume risk is only present during close contact or aerosol generating procedures, but studies show intermittent use of respirators is not protective. New research in aerosol science confirms the risk of infection is widespread in health facilities. In community settings, any mask use is protective during epidemics, especially if used early, when combined with hand hygiene, and if wearers are compliant. Community use of N95 respirators is more protective than surgical masks, which are more protective than cloth masks, but even cloth masks provide some protection. Mask guidelines should be adaptable to the specific context and should account for rising epidemic activity, and whether a pathogen has asymptomatic transmission. The main rationale for universal masking during pandemics is asymptomatic transmission, which means risk of transmission cannot be self-identified. The precautionary principle should be applied during serious emerging infections or pandemics when transmission mode is not fully understood, or vaccines and drugs are not available. If respirators are not available, medical or cloth masks could be used as a last resort. Data exist to support extended use and reuse of masks and respirators during short supply. In summary, extensive evidence generated during the covid-19 pandemic confirms the superiority of respirators and supports the use of masks and respirators in the community during periods of high epidemic activity. Some gaps in research remain, including economic analyses, research in special population groups for whom masking is challenging, and research on countering disinformation.

Comparison of the incidence and risk factors of COVID-19 and influenza associated acute respiratory illnesses: Results of the SHIVERS-II, III, IV prospective community cohort study

BACKGROUND

While severe outcomes among hospitalised patients with COVID-19 and influenza are well described, comparative studies on community transmission and milder illnesses associated with COVID-19 and influenza are lacking.

METHODS

We compared incidence, risk/protective factors, and clinical features among prospective community cohort participants with PCR-confirmed COVID-19-associated and influenza-associated acute respiratory illnesses (ARI) from 7-February to 2-October 2022 in Wellington, New Zealand.

FINDINGS

The crude COVID-19-associated ARI incidence was 59/100 person-years (PY). The adjusted cumulative incidence for COVID-19 [77/100-PY;95%CI,75-80] was 4.5 times higher than for influenza [17/100-PY;95%CI,15-19]. The proportion of children (0-17 years) with COVID-19 of all COVID-19 cases was substantial but smaller than those of influenza [402/1229 (33%) vs 173/255 (68%), p<0.0001]. The highest incidence of COVID-19 was among adolescents (12-17 years) [109/100-PY;95%CI,97-119] and non-Māori/Pacific [83/100-PY;95%CI,80-86] whereas the highest influenza incidence was among children (1-4 years) [49/100-PY;95%CI,40-58] and Māori [35/100-PY;95%CI,28-43].Adolescents (12-17 years) had 2.5 times higher peak COVID-19 incidence (5.9/100) than adults ≥18 years (2.4/100). Adolescents with two doses of the COVID-19 vaccines had 75% greater risk of COVID-19 infection [hazard ratio:1.75,95%CI,1.40-2.20] compared to adults with three doses.Vaccination, age, ethnicity, and household size were independent protective/risk factors for COVID-19 or influenza.Participants with COVID-19, compared with influenza, were less likely to access healthcare or experience febrile/severe illnesses, but more likely to report sore throat, headache, myalgia, and taste/smell loss.

INTERPRETATION

As the world transitions to COVID-19 endemicity, estimating disease burdens in community settings becomes important to understand complete disease pyramids, risk factors and clinical progression for informing countermeasures.

Impact of disease severity, age, sex, comorbidity, and vaccination on secondary attack rates of SARS-CoV-2: a global systematic review and meta-analysis

BACKGROUND

Understanding the key drivers of SARS-CoV-2 transmission is essential for shaping effective public health strategies. However, transmission risk is subject to substantial heterogeneity related to disease severity, age, sex, comorbidities, and vaccination status in different population settings and regions. We aimed to quantify the impact of these factors on secondary attack rates (SARs) of SARS-CoV-2 across diverse population settings and regions, and identify key determinants of transmission to inform targeted interventions for improving global pandemic response.

METHODS

To retrieve relevant literature covering the duration of the COVID-19 pandemic, we searched Ovid MEDLINE, Ovid Embase, Web of Science, and the Cochrane COVID-19 Study Register between January 1, 2020 and January 18, 2024 to identify studies estimating SARs of SARS-CoV-2, defined as the proportion of close contacts infected. We pooled SAR estimates using a random-effects model with the Freeman-Tukey double arcsine transformation and derived Clopper-Pearson 95% confidence intervals (CIs). Risk of bias was assessed using a modified Newcastle-Ottawa scale. This study was registered with PROSPERO, CRD42024503782.

RESULTS

A total of 159 eligible studies, involving over 19 million close contacts and 6.8 million cases from 41 countries across five continents, were included in the analysis. SARs increased with disease severity in index cases, ranging from 0.10 (95% CI: 0.06-0.14; I2 = 99.65%) in asymptomatic infection to 0.15 (95% CI: 0.09-0.21; I2 = 92.49%) in those with severe or critical conditions. SARs by age were lowest at 0.20 (95% CI: 0.16-0.23; I2 = 99.44%) for close contacts under 18 years and highest at 0.29 (95% CI: 0.24-0.34; I2 = 99.65%) for index cases aged 65 years or older. Among both index cases and close contacts, pooled SAR estimates were highest for Omicron and lowest for Delta, and declined with increasing vaccine doses. Regionally, North America had the highest SAR at 0.27 (95% CI: 0.24-0.30; I2 = 99.31%), significantly surpassing SARs in Europe (0.19; 95% CI: 0.15-0.25; I2 = 99.99%), Southeast Asia (0.18; 95% CI: 0.13-0.24; I2 = 99.24%), and the Western Pacific (0.11; 95% CI: 0.08-0.15; I2 = 99.95%). Among close contacts with comorbidities, chronic lung disease and hypertension were associated with the highest SARs. No significant association was found between SARs and the sex of either index cases or close contacts.

CONCLUSIONS

Secondary attack rates varied substantially by demographic and regional characteristics of the studied populations. Our findings demonstrate the role of booster vaccinations in curbing transmission, underscoring the importance of maintaining population immunity as variants of SARS-CoV-2 continue to emerge. Effective pandemic responses should prioritise tailored interventions that consider population demographics and social dynamics across different regions.

Immune responses to SARS-CoV-2 in sub-Saharan Africa and western Europe: a retrospective, population-based, cross-sectional study

BACKGROUND

SARS-CoV-2 has been associated with a higher proportion of asymptomatic infections and lower mortality in sub-Saharan Africa than high-income countries. However, there is currently a lack of data on cellular immune responses to SARS-CoV-2 in people living in Africa compared with people in high-income regions of the world. We aimed to assess geographical variation in peripheral and mucosal immune responses.

METHODS

In this retrospective, population-based, cross-sectional study, we analysed peripheral blood and nasal curettage samples from seven clinical studies involving individuals from Senegal (Senegalese cohort), the Netherlands, and Germany (European cohort). Samples were collected between Nov 1, 2018, and Dec 20, 2021. We included samples from individuals with no, mild, or severe COVID-19. A validation cohort of individuals from Senegal and Gabon (n=64) was used to validate key findings from the main cohort. Matching of individuals between geographical regions by age, sex, viral load, and infection severity and duration was used to address confounding factors. We examined the cellular, humoral, and cytokine immune responses using cytometry by time of flight, spectral flow cytometry, ELISA, and Luminex.

FINDINGS

We included 133 individuals (59 from the Senegalese cohort and 74 from the European cohort). In contrast to the European cohort, mild COVID-19 in the Senegalese cohort was not associated with any statistically significant perturbations in blood or nasal immune cell profiles, nor with increased pro-inflammatory cytokines, although SARS-CoV-2-specific adaptive immunity was readily induced, as seen in Europeans. In severe COVID-19, both the Senegalese and European cohorts showed lymphopenia (Senegal: 2·9-times decrease, p=0·0010 vs Europe: 1·6-times decrease, p=0·0046) and increased neutrophil frequencies in blood (Senegal: 2·0-times increase, p=0·0044 vs Europe: 1·3-times increase, p=0·026) and the nasal mucosa CD66b+CD16low neutrophils (Senegal: 9·9-times increase, p=0·045 vs Europe: 392-times increase, p<0·0001). However, in contrast to Europeans, the Senegalese cohort had no significant expansion of immature immune populations, inflammasome activation, or monocyte recruitment to the nasal mucosa.

INTERPRETATION

The observed divergent immunological trajectories during SARS-CoV-2 infection offer a potential explanation for the reported attenuated disease course in sub-Saharan Africa and highlight the need to further investigate immune responses to SARS-CoV-2 in understudied populations.

FUNDING

European and Developing Countries Clinical Trials Partnership 2 programme (AIDCO), LUMC Gisela Thier Fellowship, Dutch Research Council (NWO), European Research Council, and Leids Universitair Fonds.

A retrospective cohort study on COVID-19 reinfections and associated factors during six waves of the pandemic in Mexico

BACKGROUND

Monitoring reinfections helps predict peaks, variant emergence, and immunity trends. While reinfection rates between 3 and 31 % have been reported, a better understanding of their variation in different geographical areas could guide prevention and vaccination efforts.

AIMS

This study examines the incidence of COVID-19 reinfection and associated factors in Mexico over six pandemic waves. Rapid mutation of SARS-CoV-2 generates variants that affect reinfection rates and population immunity.

METHODS

In this retrospective cohort study, data from 3,236,259 primary infections were analyzed, and 212,892 reinfections were identified.

RESULTS

Sex, age, vaccination status, and initial infection severity were found to be significant predictors of reinfection. Furthermore, the risk of reinfection decreased with wave progression, especially for those infected during the first wave. Reduced risk of reinfection after hospitalization suggests improved exposure prevention. Results indicated increased reinfection rates during the Omicron wave, particularly for those who were originally infected during the first wave, with women and middle-aged groups at higher risk.

CONCLUSIONS

Our results highlight the intricate relationship between viral evolution, immunity, and demographics, which is crucial for effective pandemic management and vaccination strategies.

Single-cell multiomics reveal divergent effects of DNMT3A- and TET2-mutant clonal hematopoiesis in inflammatory response

ABSTRACT

DNMT3A and TET2 are epigenetic regulator genes commonly mutated in age-related clonal hematopoiesis (CH). Despite having opposed epigenetic functions, these mutations are associated with increased all-cause mortality and a low risk for progression to hematologic neoplasms. Although individual impacts on the epigenome have been described using different model systems, the phenotypic complexity in humans remains to be elucidated. Here, we make use of a natural inflammatory response occurring during coronavirus disease 2019 (COVID-19), to understand the association of these mutations with inflammatory morbidity (acute respiratory distress syndrome [ARDS]) and mortality. We demonstrate the age-independent, negative impact of DNMT3A mutant (DNMT3Amt) CH on COVID-19-related ARDS and mortality. Using single-cell proteogenomics we show that DNMT3A mutations involve myeloid and lymphoid lineage cells. Using single-cell multiomics sequencing, we identify cell-specific gene expression changes associated with DNMT3A mutations, along with significant epigenomic deregulation affecting enhancer accessibility, resulting in overexpression of interleukin-32 (IL-32), a proinflammatory cytokine that can result in inflammasome activation in monocytes and macrophages. Finally, we show with single-cell resolution that the loss of function of DNMT3A is directly associated with increased chromatin accessibility in mutant cells. Hence, we demonstrate the negative prognostic impact of DNMT3Amt CH on COVID-19-related ARDS and mortality. DNMT3Amt CH in the context of COVID-19, was associated with inflammatory transcriptional priming, resulting in overexpression of IL32. This overexpression was secondary to increased chromatic accessibility, specific to DNMT3Amt CH cells. DNMT3Amt CH can thus serve as a potential biomarker for adverse outcomes in COVID-19.

Autoantibodies in COVID-19: implications for disease severity and clinical outcomes

Few pathogens have historically been subjected to as intense scientific and clinical scrutiny as SARS-CoV-2. The genetic, immunological, and environmental factors influencing disease severity and post-infection clinical outcomes, known as correlates of immunity, remain largely undefined. Clinical outcomes of SARS-CoV-2 infection vary widely, ranging from asymptomatic cases to those with life-threatening COVID-19 symptoms. While most infected individuals return to their former health and fitness within a few weeks, some develop debilitating chronic symptoms, referred to as long-COVID. Autoimmune responses have been proposed as one of the factors influencing long-COVID and the severity of SARS-CoV-2 infection. The association between viral infections and autoimmune pathologies is not new. Viruses such as Epstein-Barr virus and cytomegalovirus, among others, have been shown to induce the production of autoantibodies and the onset of autoimmune conditions. Given the extensive literature on SARS-CoV-2, here we review current evidence on SARS-CoV-2-induced autoimmune pathologies, with a focus on autoantibodies. We closely examine mechanisms driving autoantibody production, particularly their connection with disease severity and long-COVID.

Dynamic modeling of antibody repertoire reshaping in response to viral infections

For decades, research has largely focused on the generation of high-affinity, antigen-specific antibodies during viral infections. This emphasis has made it challenging for immunologists to systematically evaluate the mechanisms initiating humoral immunity in specific immune responses. In this study, we employ ordinary differential equations (ODE) to investigate the dynamic reshaping of the entire antibody repertoire in response to viral infections. Our findings demonstrate that the host's antibody atlas undergoes significant restructuring during these infections by the selective expansion of antibody pools with strong binding activity. The simulation results indicate that the ELISA (Enzyme-Linked Immunosorbent Assay) outcomes do not directly reflect the levels of specific neutralizing antibodies, but rather represent a quantitative response of the reshaped antibody repertoire following infection. Our model transcends traditional theories of immune memory, providing an explanation for the sustained presence of specific antibodies in the human body in long term. Additionally, our model extends to explore the mechanistic basis of the original antigenic sin, providing practical applications of our framework. One important application of this model is that it indicates that antibodies with a faster forward binding rate are more effective in preventing and treating associated viral infections compared to those with higher binding affinity.

Occupational and non-occupational factors of post-COVID-19 condition: a cross-sectional survey in the French general working population

Introduction

Although the working population carries the greatest burden of long COVID, occupational and non-occupational factors of the condition have not yet been well documented in this population. The aim of this study was to investigate these factors.

Methods

A nationwide random sampling cross-sectional survey was conducted among the adult population in mainland France after the large Omicron waves in the autumn of 2022. Post-COVID-19 condition (PCC) was defined according to the WHO. Associations of occupational and non-occupational factors with PCC were tested in a conceptual model accounting for the relationships between these factors and considering two control groups (previously infected participants without PCC and participants with no reported or diagnosed SARS-CoV-2 infection). Interactions between occupational and non-occupational factors were considered.

Results

The survey included 1131 working adults. PCC was positively associated with reported infection while providing care (prevalence ratio (PR)=2.06 (95% CI 1.08 to 3.94)), being in contact with a colleague (PR=1.61 (95% CI 1.04 to 2.48)) and increased workload (PR=2.85 (95% CI 1.12 to 7.24)), whereas it was negatively associated with reported infection while being in contact with the public or clients (PR=0.23 (95% CI 0.07 to 0.76)). Several non-occupational factors were associated with PCC: sex, household size, household financial satisfaction, number of pre-existing chronic conditions, anxiety, injury sequelae and perceived SARS-CoV-2 infection severity. No interactions were found between these factors.

Conclusions

Reducing the burden of long COVID in the working population requires public health strategies that consider a wide spectrum of factors, including work conditions in a broad sense. Specific attention should be given to the most vulnerable workers accumulating such factors.

The Second Round of a Population-Based Seroprevalence Study of Anti-SARS-CoV-2 Antibodies and COVID-19 Vaccination Assessment in the Republika Srpska, Bosnia and Herzegovina

INTRODUCTION

The aim of the study was to assess the seroprevalence of SARS-CoV-2 in the Republika Srpska, Bosnia and Herzegovina, after five waves of COVID-19 and 1 year after introduction of vaccination to better understand the true extent of the COVID-19 pandemic in the population of the Republika Srpska and role of vaccination in achieving herd immunity.

METHODS

The population-based study was conducted from December 2021 to February 2022 in a group of 4463 individuals in the Republika Srpska. Total anti-SARS-CoV-2 antibodies were determined in serum specimens using the Wantai total antibody ELISA assay. Quantitative analysis, using Kantaro IgG assays, was performed in subsamples (1273 specimens) to asses and compare levels of IgG among vaccinated, recovered and participants with hybrid immunity. To adjust for age and gender distribution in sample, poststratification method is applied.

RESULTS

The overall cumulative seroprevalence was 94.6% (95% CI = 93.9-95.3). Significantly higher seroprevalence rates were observed among vaccinated 97.8% (95% CI = 97.3-98.4) comparing to unvaccinated participants (89.5%, 95% CI = 88.0-91.0). Seroprevalence increases with the number of received doses. Among various professions, the highest seroprevalence was found in the service industry (98.1%), education (98.0%) and healthcare (96.9%). We found that 2.2% of vaccinated and 3.6% of participants with SARS-CoV-2 positivity during 2021 had no detectable IgG antibodies. Both seroprevalence (98.6%) and antibody titres (1094.4 AU/mL) were significantly higher among people with hybrid immunity.

CONCLUSION

Our findings reveal a 2.3-fold increase in seroprevalence of SARS-CoV-2 antibodies due to infection and vaccination, comparing to the first study performed 1 year earlier. This study provides better understanding of the SARS-CoV-2 transmission and highlights the important role of the vaccination in achieving the population immunity. Periodically conducted population-based seroprevalence studies are important to understand temporal trends and assess surveillance system performance and public compliance with vaccination policies.

Long COVID in the Belgian Defence forces: prevalence, risk factors and impact on quality of daily functioning

INTRODUCTION

Long COVID (LC) is a medical condition first described and documented through anecdotes on social media by patients prior to being recognised by WHO as a disease. Although >50 prolonged symptoms of LC have been described, it remains a diagnostic challenge for military providers and therefore threatens operational readiness.

METHODS

On 9 September 2021, an online survey was emailed to 2192 Belgian Defence personnel who had previously tested PCR positive for SARS-CoV-2 between 17 August 2020 and 31 May 2021. A total of 718 validated responses were received.Descriptive analyses determined the prevalence of LC and 10 most common symptoms and their duration following infection. In the explanatory analyses, risk factors related to LC were identified. To establish the health-related impact of LC on quality of life (HRQoL), we used the results from the EuroQol 5 Dimension 5 Level questionnaire.

RESULTS

The most frequent symptoms that were reported for >3 months were fatigue, lack of energy and breathing difficulties.47.35% of the respondents reported at least one persistent symptom, while 21.87% reported more than 3 symptoms lasting for at least 3 months after the initial COVID-19 infection. Most patients with LC suffered from symptoms of a neuropsychiatric nature (71.76%).LC was significantly associated with obesity; pre-existing respiratory disease and blood or immune disorders. Physical activity of >3 hours per week halved the risk of LC.The total QoL is reduced in patients with LC. Considering the five dimensions of the questionnaire, only the self-care dimension was not influenced by the presence of LC.

CONCLUSIONS

Almost half of Belgian Defence personnel developed LC after a confirmed COVID-19 infection, similar to numbers found in the Belgian population. Patients with LC would likely benefit from a multidisciplinary rehabilitation approach that addresses shortness of breath, fatigue and mood disturbance.

Hearing Loss in COVID-19 Patients: An Audiological Profile of Symptomatic and Asymptomatic COVID-19 Patients in Qatar

Background and objective Viral infections caused by cytomegalovirus, lymphocytic choriomeningitis virus, varicella-zoster virus, herpes simplex type 1 and type 2, rubella, measles, rubeola, HIV, West Nile virus, Lassa virus, and mumps are known to be associated with hearing loss. There have been reports of inner ear involvement in coronavirus disease 2019 (COVID-19) patients but the extent and variations in cochlear involvement of symptomatic and asymptomatic patients has not been adequately described. This study aimed to evaluate the hearing status among symptomatic and asymptomatic COVID-19 patients to address the prospects for routine screening for hearing loss in COVID-19 patients. Methods Patients testing positive for COVID-19 between March 2020 and May 2020 and August 2020 and October 2020 in Qatar were screened. A total of 110 patients aged 15-50 years were enrolled and grouped into symptomatic and asymptomatic COVID-19 after telephonic screening. Of them, seven were excluded for various reasons. A questionnaire was administered in person to all included participants. Audiological testing results of symptomatic and asymptomatic patients were analyzed. Results Of the 103 patients included in the study, 49 were symptomatic and 54 asymptomatic; 15 (14.6 %) had high-frequency sensorineural hearing loss (SNHL) in one or both ears. Mean thresholds in extended high frequencies 10K-20K were higher in symptomatic patients. Abnormal distortion product otoacoustic emissions (DPOAEs) were seen in 40 (38.8%) patients; 63.3% (31/49) were symptomatic and 16.7% (9/54) were asymptomatic in 3K-8K frequencies (p=0.0001).  Conclusions Symptomatic COVID-19 patients had significant involvement of the inner ears with abnormal pure tone audiometry (PTA), extended high-frequency audiometry (EHFA), and DPOAEs compared to asymptomatic COVID-19 patients. The extent of inner-ear involvement suggests the severity of the infection. The lack of audiovestibular symptoms does not rule out normal hearing in such patients. Screening for hearing loss should be routinely considered in post-COVID-19 patients.

A novel comparison framework for epidemiological strategies applied to age-based restrictions versus horizontal lockdowns

During an epidemic, such as the COVID-19 pandemic, policy-makers are faced with the decision of implementing effective, yet socioeconomically costly intervention strategies, such as school and workplace closure, physical distancing, etc. In this study, we propose a rigorous definition of epidemiological strategies. In addition, we develop a scheme for comparing certain epidemiological strategies, with the goal of providing policy-makers with a tool for their systematic comparison. Then, we put the suggested scheme to the test by employing an age-based epidemiological compartment model introduced in Bitsouni et al. (2024), coupled with data from the literature, in order to compare the effectiveness of age-based and horizontal interventions. In general, our findings suggest that these two are comparable, mainly at a low or medium level of intensity.

Measurement of circulating viral antigens post-SARS-CoV-2 infection in a multicohort study

OBJECTIVES

To determine the proportion of individuals with detectable antigen in plasma or serum after SARS-CoV-2 infection and the association of antigen detection with postacute sequelae of COVID-19 (PASC) symptoms.

METHODS

Plasma and serum samples were collected from adults participating in four independent studies at different time points, ranging from several days up to 14 months post-SARS-CoV-2 infection. The primary outcome measure was to quantify SARS-CoV-2 antigens, including the S1 subunit of spike, full-length spike, and nucleocapsid, in participant samples. The presence of 34 commonly reported PASC symptoms during the postacute period was determined from participant surveys or chart reviews of electronic health records.

RESULTS

Of the 1569 samples analysed from 706 individuals infected with SARS-CoV-2, 21% (95% CI, 18-24%) were positive for either S1, spike, or nucleocapsid. Spike was predominantly detected, and the highest proportion of samples was spike positive (20%; 95% CI, 18-22%) between 4 and 7 months postinfection. In total, 578 participants (82%) reported at least one of the 34 PASC symptoms included in our analysis ≥1 month postinfection. Cardiopulmonary, musculoskeletal, and neurologic symptoms had the highest reported prevalence in over half of all participants, and among those participants, 43% (95% CI, 40-45%) on average were antigen-positive. Among the participants who reported no ongoing symptoms (128, 18%), antigen was detected in 28 participants (21%). The presence of antigen was associated with the presence of one or more PASC symptoms, adjusting for sex, age, time postinfection, and cohort (OR, 1.8; 95% CI, 1.4-2.2).

DISCUSSION

The findings of this multicohort study indicate that SARS-CoV-2 antigens can be detected in the blood of a substantial proportion of individuals up to 14 months after infection. While approximately one in five asymptomatic individuals was antigen-positive, roughly half of all individuals reporting ongoing cardiopulmonary, musculoskeletal, and neurologic symptoms were antigen-positive.

SARS-CoV-2 infection prevalence, risk factors, and outcomes among non-clinical-related service providers in a national healthcare system

Health care workers (HCWs) may be at a variable risk of SARS-CoV2 infection. Regardless of their involvement in providing direct clinical treatment, most of the prior research had included all HCWs. Understanding infection rates, risk factors and outcomes among different subgroups of HCWs is crucial. From February 28, 2020 to January 1, 2022, we conducted a retrospective analysis encompassing all full-time non-clinical staff (NCS) subcontracted with Hamad Medical Corporation (HMC) facilities. To determine current or previous SARS-CoV2 infection, all personnel underwent RT-PCR and/or serology testing. To identify the demographic factors linked to the risk of infection, we utilized Cox-Hazard regression analysis. Herein 3158/6231 (50.7%) subcontracted NCS tested positive for SARS-CoV-2 by RT-PCR or serology during the research period. The median age was 30 years (IQR 25,35), 69.8% of the population were males, 82.4% were from South Asia, 86.6% did not have any concomitant conditions. 6032 (96.8%) of the population lived in shared housing, while 4749 (76.2%) had low to median levels of education. While infection (PCR positive with or without seropositive results) was independently predicted by male gender, working in the catering, laundry, and security sectors and being intermediate (7-12 years of education), lower (0-6 years of education), higher (exposure to confirmed case), and having symptoms. Male gender, working in the security sectors and being intermediate (7-12 years of education) were independently associated with accidently detected cases (PCR negative and seropositive). 299 (4.8%) required hospitalization, of them 3 cases were severe pneumonia and one required ICU admission without mechanical ventilation, with no deaths reported. In conclusion Infection rates among NCS are high. The majority are asymptomatic and may contribute to ongoing illness spread in the public or in healthcare facilities. During a pandemic, routine screening of this population is crucial and may aid in containing the spread of infection.

Public health and economic impact of COVID-19 vaccination with the Pfizer-BioNTech COVID-19 Vaccine, KP.2, among adults in 2024/2025 in the United States

OBJECTIVES

To assess the public health and economic impact of vaccination with the Pfizer-BioNTech COVID-19 vaccine, KP.2, in 2024/2025 in the United States.

METHODS

A combined cohort Markov-decision tree model was used to estimate the cost-effectiveness and budget impact of vaccination versus no vaccination in adults aged ≥18 years. The adult population was further stratified into 18-64 years and ≥65 years age groups. Public health surveillance data informed the annual proportion of individuals infected with and vaccinated against SARS-CoV-2 and the proportion of those infected who were hospitalized, stratified by age. Other age-stratified clinical, cost, and vaccine effectiveness parameters were informed by literature. The budget impact analysis was based on a hypothetical 1-million-member plan and used a payer perspective. Parameter uncertainty was tested in sensitivity analyses.

RESULTS

Without vaccination, the model projected 21.4 million new symptomatic cases, 15,793 deaths, 629,098 hospitalizations, $115.5 billion in total costs, and 1 million QALYs lost among adults aged ≥18 years, with the greatest health burden observed among older adults aged ≥65 years (72% of hospitalizations and 86% of deaths) and the greatest economic burden in adults aged 18 to 64 years (62% of total costs). Vaccination was projected to prevent 915,501 cases, 1,057 deaths, and 37,489 hospitalizations, resulting in cost savings of $513 million, 9,173 LYs gained, 56,482 QALYs gained, and a dominant ICER. In the budget impact analysis, vaccination was estimated to result in total incremental cost savings for the population aged ≥ 65 years and a modest budget increase for the population aged 18 to 64 years.

CONCLUSIONS

Vaccination with the Pfizer BioNTech COVID-19 vaccine, KP.2, is a cost-effective measure from the societal perspective at a willingness-to-pay threshold of $50,000 that could reduce the health and economic burden of COVID-19.

Tracking inflammation resolution signatures in lungs after SARS-CoV-2 omicron BA.1 infection of K18-hACE2 mice

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19), which can result in severe disease, often characterised by a 'cytokine storm' and the associated acute respiratory distress syndrome. However, many infections with SARS-CoV-2 are mild or asymptomatic throughout the course of infection. Although blood biomarkers of severe disease are well studied, less well understood are the inflammatory signatures in lung tissues associated with mild disease or silent infections, wherein infection and inflammation are rapidly resolved leading to sequelae-free recovery. Herein we described RNA-Seq and histological analyses of lungs over time in an omicron BA.1/K18-hACE2 mouse infection model, which displays these latter features. Although robust infection was evident at 2 days post infection (dpi), viral RNA was largely cleared by 10 dpi. Acute inflammatory signatures showed a slightly different pattern of cytokine signatures compared with severe infection models, and where much diminished 30 dpi and absent by 66 dpi. Cellular deconvolution identified significantly increased abundance scores for a number of anti-inflammatory pro-resolution cell types at 5/10 dpi. These included type II innate lymphoid cells, T regulatory cells, and interstitial macrophages. Genes whose expression trended downwards over 2-66 dpi included biomarkers of severe disease and were associated with 'cytokine storm' pathways. Genes whose expression trended upward during this period were associated with recovery of ciliated cells, AT2 to AT1 transition, reticular fibroblasts and innate lymphoid cells, indicating a return to homeostasis. Very few differentially expressed host genes were identified at 66 dpi, suggesting near complete recovery. The parallels between mild or subclinical infections in humans and those observed in this BA.1/K18-hACE2 mouse model are discussed with reference to the concept of "protective inflammation".

Genomic surveillance of Canadian airport wastewater samples allows early detection of emerging SARS-CoV-2 lineages

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown wastewater (WW) surveillance to be an effective means of tracking the emergence of viral lineages which arrive by many routes of transmission including via transportation hubs. In the Canadian province of Ontario, numerous municipal wastewater treatment plants (WWTPs) participate in WW surveillance of infectious disease targets such as SARS-CoV-2 by qPCR and whole genome sequencing (WGS). The Greater Toronto Airports Authority (GTAA), operator of Toronto Pearson International Airport (Toronto Pearson), has been participating in WW surveillance since January 2022. As a major international airport in Canada and the largest national hub, this airport is an ideal location for tracking globally emerging SARS-CoV-2 variants of concern (VOCs). In this study, WW collected from Toronto Pearson's two terminals and pooled aircraft sewage was processed for WGS using a tiled-amplicon approach targeting the SARS-CoV-2 virus genome. Data generated was analyzed to monitor trends of SARS-CoV-2 lineage frequencies. Initial detections of emerging lineages were compared between Toronto Pearson WW samples, municipal WW samples collected from the surrounding regions, and Ontario clinical data as published by Public Health Ontario. Results enabled the early detection of VOCs and individual mutations emerging in Ontario. On average, the emergence of novel lineages at the airport preceded clinical detections by 1-4 weeks, and up to 16 weeks in one case. This project illustrates the efficacy of WW surveillance at transitory transportation hubs and sets an example that could be applied to other viruses as part of a pandemic preparedness strategy and to provide monitoring on a mass scale.

Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater

OBJECTIVES

Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study aimed to monitor the SARS-CoV-2 variant community dynamics and evolution using receptor-binding domain (RBD) amplicon sequencing of wastewater samples.

METHODS

We sequenced wastewater from El Paso, Texas, over 17 months, compared the sequencing data with clinical genome data, and performed biodiversity analysis to reveal SARS-CoV-2 variant dynamics and evolution.

RESULTS

We identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Comparison with clinical genome sequencing data revealed earlier detection of variants and identification of unreported outbreaks. Our results also showed strong consistency with clinical data for dominant variants at the local, state, and national levels. Alpha diversity analyses revealed significant seasonal variations, with the highest diversity observed in winter. By segmenting the outbreak into lag, growth, stationary, and decline phases, we found higher variant diversity during the lag phase, likely due to lower inter-variant competition preceding outbreak growth.

CONCLUSIONS

Our findings underscore the importance of low transmission periods in facilitating rapid mutation and variant evolution. Our approach, integrating RBD amplicon sequencing with wastewater surveillance, demonstrates effectiveness in tracking viral evolution and understanding variant emergence, thus enhancing public health preparedness.

SARS-CoV-2 anti-N antibodies among healthcare personnel without previous known COVID-19

Objective

To measure SARS-CoV-2 anti-nucleocapsid (anti-N) antibody seropositivity among healthcare personnel (HCP) without a history of COVID-19 and to identify HCP characteristics associated with seropositivity.

Design

Prospective cohort study from September 22, 2020, to March 3, 2022.

Setting

A tertiary care academic medical center.

Participants

727 HCP without prior positive SARS-CoV-2 PCR testing were enrolled; 559 HCP successfully completed follow-up.

Methods

At enrollment and follow-up 1-6 months later, HCP underwent SARS-CoV-2 anti-N testing and were surveyed on demographics, employment information, vaccination status, and COVID-19 symptoms and exposures.

Results

Of 727 HCP enrolled, 27 (3.7%) had a positive SARS-CoV-2 anti-N test at enrollment. Seropositive HCPs were more likely to have a household exposure to COVID-19 in the past 30 days (OR 7.92, 95% CI 2.44-25.73), to have had an illness thought to be COVID-19 (4.31, 1.94-9.57), or to work with COVID-19 patients more than half the time (2.09, 0.94-4.77). Among 559 HCP who followed-up, 52 (9.3%) had a positive SARS-CoV-2 anti-N antibody test result. Seropositivity at follow-up was associated with community/household exposures to COVID-19 within the past 30 days (9.50, 5.02-17.96; 2.90, 1.31-6.44), having an illness thought to be COVID-19 (8.24, 4.44-15.29), and working with COVID-19 patients more than half the time (1.50, 0.80-2.78).

Conclusions

Among HCP without prior positive SARS-CoV-2 testing, SARS-CoV-2 anti-N seropositivity was comparable to that of the general population and was associated with COVID-19 symptomatology and both occupational and non-occupational exposures to COVID-19.

SARS-CoV-2 infection and the risk of depressive symptoms: a retrospective longitudinal study from the population-based CONSTANCES cohort

BACKGROUND

Should COVID-19 have a direct impact on the risk of depression, it would suggest specific pathways for prevention and treatment. In this retrospective population-based study, we aimed to examine the association of prior SARS-CoV-2 infection with depressive symptoms, distinguishing self-reported v. biologically confirmed COVID-19.

METHODS

32 007 participants from the SAPRIS survey nested in the French CONSTANCES cohort were included. COVID-19 was measured as followed: ad hoc serologic testing, self-reported PCR or serology positive test results, and self-reported COVID-19. Depressive symptoms were measured with the Center of Epidemiologic Studies-Depression Scale (CES-D). Outcomes were depressive symptoms (total CES-D score, its four dimensions, and clinically significant depressive symptoms) and exposure was prior COVID-19 (no COVID-19/self-reported unconfirmed COVID-19/biologically confirmed COVID-19).

RESULTS

In comparison to participants without COVID-19, participants with self-reported unconfirmed COVID-19 and biologically confirmed COVID-19 had higher CES-D scores (β for one interquartile range increase [95% CI]: 0.15 [0.08-0.22] and 0.09 [0.05-0.13], respectively) and somatic complaints dimension scores (0.15 [0.09-0.21] and 0.10 [0.07-0.13]). Only those with self-reported but unconfirmed COVID-19 had higher depressed affect dimension scores (0.08 [0.01-0.14]). Accounting for ad hoc serologic testing only, the CES-D score and the somatic complaints dimension were only associated with the combination of self-reported COVID-19 and negative serology test results.

CONCLUSIONS

The association between COVID-19 and depressive symptoms was merely driven by somatic symptoms of depression and did not follow a gradient consistent with the hypothesis of a direct impact of SARS-CoV-2 infection on the risk of depression.

Longitudinal wastewater-based surveillance of SARS-CoV-2 during 2023 in Ethiopia

Introduction

Although wastewater-based epidemiology (WBE) successfully functioned as a tool for monitoring the coronavirus disease 2019 (COVID-19) pandemic globally, relatively little is known about its utility in low-income countries. This study aimed to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater, estimate the number of infected individuals in the catchment areas, and correlate the results with the clinically reported COVID-19 cases in Addis Ababa, Ethiopia.

Methods

A total of 323 influent and 33 effluent wastewater samples were collected from three Wastewater Treatment Plants (WWTPs) using a 24-h composite Moore swab sampling method from February to November 2023. The virus was captured using Ceres Nanotrap® Enhancement Reagent 2 and Nanotrap® Microbiome A Particles, and then nucleic acids were extracted using the Qiagen QIAamp Viral RNA Mini Kit. The ThermoFisher TaqPath™ COVID-19 kit was applied to perform real-time reverse transcriptase polymerase chain reaction (qRT-PCR) to quantify the SARS-CoV-2 RNA. Wastewater viral concentrations were normalized using flow rate and number of people served. In the sampling period, spearman correlation was used to compare the SARS-CoV-2 target gene concentration to the reported COVID-19 cases. The numbers of infected individuals under each treatment plant were calculated considering the target genes' concentration, the flow rate of treatment plants, a gram of feces per person-day, and RNA copies per gram of feces.

Results

SARS-CoV-2 was detected in 94% of untreated wastewater samples. All effluent wastewater samples (n = 22) from the upflow anaerobic sludge blanket (UASB) reactor and membrane bioreactor (MBR) technology were SARS-COV-2 RNA negative. In contrast, two out of 11 effluents from Waste Stabilization Pond were found positive. Positive correlations were observed between the weekly average SARS-CoV-2 concentration and the cumulative weekly reported COVID-19 cases in Addis Ababa. The estimated number of infected people in the Kality Treatment catchment area was 330 times the number of COVID-19 cases reported during the study period in Addis Ababa.

Discussion

This study revealed that SARS-CoV-2 was circulating in the community and confirmed previous reports of more asymptomatic COVID-19 cases in Ethiopia. Additionally, this study provides further evidence of the importance of wastewater-based surveillance in general to monitor infectious diseases in low-income settings.

Conclusion

Wastewater-based surveillance of SARS-CoV-2 can be a useful method for tracking the increment of COVID-19 cases before it spreads widely throughout the community.

Sick leave due to SARS-CoV-2 infection

BACKGROUND

Coronavirus disease 2019 (COVID-19) caused a high burden of sick leave worldwide. Long-term sick leave for COVID-19 may be longer than for other influenza-like syndromes. The real impact of long COVID on absenteeism remains uncertain.

AIMS

To investigate the burden of sick leave, especially >12 weeks, in Belgian workers with a positive polymerase chain reaction (PCR) test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from July 2020 to September 2021 and to compare these figures with sick leave for other infectious diseases.

METHODS

We coupled a database of SARS-CoV-2-positive workers and workers who were absent for other infections with objective absence data. Predictors of prolonged sickness were evaluated by negative binomial regression, Cox proportional hazards regression and ordinal logistic regression.

RESULTS

The study population involved 2569 workers who tested positive for SARS-CoV-2 and 392 workers who were absent for other infectious diseases. In total, 16% (95% CI 14-17%) of workers with a positive SARS-CoV-2 test had no sick leave registered. Fourteen out of 1000 (95% CI 9-20‰) workers with absenteeism for COVID-19 experienced sick leave >12 weeks as compared to 43 out of 1000 workers (95% CI 3-69‰) with absenteeism due to other infections. When including PCR-positive workers without sick leave, the prevalence of long-term sick leave decreased to 12 per 1000 (95% CI8-17‰). Long-term sick leave was associated with older age, high previous sick leave and low educational level.

CONCLUSIONS

The prevalence of long-term sick leave was lower than estimated in earlier investigations regardless of worrying reports about post-COVID-19 syndrome.

BCG vaccination of healthcare workers for protection against COVID-19: 12-month outcomes from an international randomised controlled trial

OBJECTIVES

Bacille Calmette-Guérin (BCG) vaccine has immunomodulatory effects that may provide protection against unrelated infectious diseases. We aimed to determine whether BCG vaccination protects adults against COVID-19.

DESIGN

Phase III double-blind randomised controlled trial.

SETTING

Healthcare centres in Australia, Brazil, the Netherlands, Spain, and the United Kingdom during the COVID-19 pandemic.

PARTICIPANTS

3988 healthcare workers with no prior COVID-19 and no contraindication to BCG.

INTERVENTION

Randomised 1:1 using a web-based procedure to receive a single 0.1 mL intradermal dose of BCG-Denmark (BCG group, n = 1999) or saline (placebo group, n = 1989).

MAIN OUTCOME MEASURES

Difference in incidence of (i) symptomatic and (ii) severe COVID-19 during the 12 months following randomisation in the modified intention to treat (mITT) population (confirmed SARS-CoV-2 naïve at inclusion).

RESULTS

Of the 3988 participants randomised, 3386 had a negative baseline SARS-CoV-2 test and were included in the mITT population. The 12-month adjusted estimated risk of symptomatic COVID-19 was higher in the BCG group (22.6%; 95% confidence interval [CI] 20.6 to 24.5%) compared with the placebo group (19.6%; 95% CI 17.6 to 21.5%); adjusted difference +3.0% points (95% CI 0.2 to 5.8%; p = 0.04). The 12-month adjusted estimated risk of severe COVID-19 (mainly comprising those reporting being unable to work for ≥3 consecutive days) was 11.0% in the BCG group (95% CI 9.5 to 12.4%) compared with 9.6% in the placebo group (95% CI 8.3 to 11.1%); adjusted difference +1.3% points (95% CI -0.7 to 3.3%, p = 0.2). Breakthrough COVID-19 (post COVID-19 vaccination) and asymptomatic SARS-CoV-2 infections were similar in the two groups. There were 18 hospitalisations due to COVID-19 (11 in BCG group, 7 in placebo group; adjusted hazard ratio 1.56, 95% CI 0.60 to 4.02, p = 0.4) and two deaths due to COVID-19, both in the placebo group.

CONCLUSIONS

Compared to placebo, vaccination with BCG-Denmark increased the risk of symptomatic COVID-19 over 12 months among healthcare workers and did not decrease the risk of severe COVID-19 or post-vaccination breakthrough COVID-19.

TRIAL REGISTRATION

ClinicalTrials.gov NCT04327206.

Endogenous hydrogen peroxide positively regulates secretion of a gut-derived peptide in neuroendocrine potentiation of the oxidative stress response in C. elegans

The gut-brain axis mediates bidirectional signaling between the intestine and the nervous system and is critical for organism-wide homeostasis. Here we report the identification of a peptidergic endocrine circuit in which bidirectional signaling between neurons and the intestine potentiates the activation of the antioxidant response in C. elegans in the intestine. We identify a FMRF-amide-like peptide, FLP-2, whose release from the intestine is necessary and sufficient to activate the intestinal oxidative stress response by promoting the release of the antioxidant FLP-1 neuropeptide from neurons. FLP-2 secretion from the intestine is positively regulated by endogenous hydrogen peroxide (H2O2) produced in the mitochondrial matrix by sod-3/superoxide dismutase, and is negatively regulated by prdx-2/peroxiredoxin, which depletes H2O2 in both the mitochondria and cytosol. H2O2 promotes FLP-2 secretion through the DAG and calciumdependent protein kinase C family member pkc-2 and by the SNAP25 family member aex-4 in the intestine. Together, our data demonstrate a role for intestinal H2O2 in promoting inter-tissue antioxidant signaling through regulated neuropeptide-like protein exocytosis in a gut-brain axis to activate the oxidative stress response.

A Brighton Collaboration standardized template with key considerations for a benefit-risk assessment for the Comirnaty COVID-19 mRNA vaccine

The Brighton Collaboration Benefit-Risk Assessment of VAccines by TechnolOgy (BRAVATO) Working Group evaluates the safety and other key features of new platform technology vaccines, including nucleic acid (RNA and DNA) vaccines. This manuscript uses the BRAVATO template to report the key considerations for a benefit-risk assessment of the coronavirus disease 2019 (COVID-19) mRNA-based vaccine BNT162b2 (Comirnaty®, or Pfizer-BioNTech COVID-19 vaccine) including the subsequent Original/Omicron BA.1, Original/Omicron BA.4-5 and Omicron XBB.1.5 variant-adapted vaccines developed by BioNTech and Pfizer to protect against COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Initial Emergency Use Authorizations or conditional Marketing Authorizations for the original BNT162b2 vaccine were granted based upon a favorable benefit-risk assessment taking into account clinical safety, immunogenicity, and efficacy data, which was subsequently reconfirmed for younger age groups, and by real world evidence data. In addition, the favorable benefit-risk assessment was maintained for the bivalent vaccines, developed against newly arising SARS-CoV-2 variants, with accumulating clinical trial data.

Susceptibility and infectiousness of SARS-CoV-2 in children versus adults, by variant (wild-type, alpha, delta): A systematic review and meta-analysis of household contact studies

IMPORTANCE

Understanding the susceptibility and infectiousness of children and adolescents in comparison to adults is important to appreciate their role in the COVID-19 pandemic.

OBJECTIVE

To determine SARS-CoV-2 susceptibility and infectiousness of children and adolescents with adults as comparator for three variants (wild-type, alpha, delta) in the household setting. We aimed to identify the effects independent of vaccination or prior infection.

DATA SOURCES

We searched EMBASE, PubMed and medRxiv up to January 2022.

STUDY SELECTION

Two reviewers independently identified studies providing secondary household attack rates (SAR) for SARS-CoV-2 infection in children (0-9 years), adolescents (10-19 years) or both compared with adults (20 years and older).

DATA EXTRACTION AND SYNTHESIS

Two reviewers independently extracted data, assessed risk of bias and performed a random-effects meta-analysis model.

MAIN OUTCOMES AND MEASURES

Odds ratio (OR) for SARS-CoV-2 infection comparing children and adolescents with adults stratified by wild-type (ancestral type), alpha, and delta variant, respectively. Susceptibility was defined as the secondary attack rate (SAR) among susceptible household contacts irrespective of the age of the index case. Infectiousness was defined as the SAR irrespective of the age of household contacts when children/adolescents/adults were the index case.

RESULTS

Susceptibility analysis: We included 27 studies (308,681 contacts), for delta only one (large) study was available. Compared to adults, children and adolescents were less susceptible to the wild-type and delta, but equally susceptible to alpha. Infectiousness analysis: We included 21 studies (201,199 index cases). Compared to adults, children and adolescents were less infectious when infected with the wild-type and delta. Alpha -related infectiousness remained unclear, 0-9 year old children were at least as infectious as adults. Overall SAR among household contacts varied between the variants.

CONCLUSIONS AND RELEVANCE

When considering the potential role of children and adolescents, variant-specific susceptibility, infectiousness, age group and overall transmissibility need to be assessed.

A serological survey of COVID-19 among predominantly aboriginal residents of a tourist island in southern Thailand

BACKGROUND

The current survey describes the seroprevalence, history of coronavirus disease 2019 (COVID-19), and vaccination status among predominantly aboriginal residents on a tourist island in southern Thailand. This information can be translated into COVID-19 vaccination and control plans for this population.

METHODS

We implemented questionnaire interviews and collected blood samples from 249 residents of Lipe Island, Satun Province, in January 2022. We measured the anti-nucleocapsid protein and anti-spike (anti-S) receptor-binding protein levels of immunoglobulin (Ig) M and IgG. The differences in antibody levels among participants with different histories of vaccination and infection were analyzed using one-way analysis of variance with multiple comparisons.

RESULTS

During the 2-year pandemic period, no island residents with COVID-19 required hospitalization despite the high prevalence of hypertension (33.3%) and diabetes mellitus (21.7%). Approximately 18.8% of the participants reported a history of COVID-19 diagnosis. In total, 95.1% of the participants had a history of complete vaccination, of which 93.5% were seropositive. The anti-S IgG geometric means (geometric standard deviation) were 3945.8 (2.0), 829.8 (9.7) AU/mL, 789.9 (5.3) AU/mL, and 22.7 (7.1) AU/mL, respectively, in participants with a history of both COVID-19 diagnosis and complete vaccination (group 1), incomplete vaccination and subsequent COVID-19 diagnosis (group 2), complete vaccination but no previous infection (group 3), or neither previous COVID-19 and complete vaccination (group 4). Significant pairwise differences in anti-S IgG levels were found between certain groups (1 vs 3, 1 vs 4, 2 vs 4, and 3 vs 4).

CONCLUSIONS

The high coverage of vaccination, high levels of population antibody titers, variable antibody levels among completely vaccinated non-infected residents, and high prevalence of non-communicable diseases (NCDs) suggested that the local health systems could control the pandemic. However, continuing surveillance, booster vaccinations, and NCD prevention programs were still required.

Mathematical assessment of the roles of age heterogeneity and vaccination on the dynamics and control of SARS-CoV-2

The COVID-19 pandemic, caused by SARS-CoV-2, disproportionately affected certain segments of society, particularly the elderly population (which suffered the brunt of the burden of the pandemic in terms of severity of the disease, hospitalization, and death). This study presents a generalized multigroup model, with m heterogeneous sub-populations, to assess the population-level impact of age heterogeneity and vaccination on the transmission dynamics and control of the SARS-CoV-2 pandemic in the United States. Rigorous analysis of the model for the homogeneous case (i.e., the model with m = 1) reveal that its disease-free equilibrium is globally-asymptotically stable for two special cases (with perfect vaccine efficacy or negligible disease-induced mortality) whenever the associated reproduction number is less than one. The model has a unique and globally-asymptotically stable endemic equilibrium, for special a case, when the associated reproduction threshold exceeds one. The homogeneous model was fitted using the observed cumulative mortality data for the United States during three distinct waves (Waves A (October 17, 2020 to April 5, 2021), B (July 9, 2021 to November 7, 2021) and C (January 1, 2022 to May 7, 2022)) chosen to align with time periods when the Alpha, Delta and Omicron were, respectively, the predominant variants in the United States. The calibrated model was used to derive a theoretical expression for achieving vaccine-derived herd immunity (needed to eliminate the disease in the United States). It was shown that, using the one-group homogeneous model, vaccine-derived herd immunity is not attainable during Wave C of the pandemic in the United States, regardless of the coverage level of the fully-vaccinated individuals. Global sensitivity analysis was carried out to determine the parameters of the model that have the most influence on the disease dynamics and burden. These analyses reveal that control and mitigation strategies that may be very effective during one wave may not be so very effective during the other wave or waves. However, strategies that target asymptomatic and pre-symptomatic infectious individuals are shown to be consistently effective across all waves. To study the impact of the disproportionate effect of COVID-19 on the elderly population, we considered the heterogeneous model for the case where the total population is subdivided into the sub-populations of individuals under 65 years of age and those that are 65 and older. The resulting two-group heterogeneous model, which was also fitted using the cumulative mortality data for wave C, was also rigorously analysed. Unlike for the case of the one-group model, it was shown, for the two-group model, that vaccine-derived herd immunity can indeed be achieved during Wave C of the pandemic if at least 61% of the populace is fully vaccinated. Thus, this study shows that adding age heterogeneity into a SARS-CoV-2 vaccination model with homogeneous mixing significantly reduces the level of vaccination coverage needed to achieve vaccine-derived herd immunity (specifically, for the heterogeneous model, herd-immunity can be attained during Wave C if a moderate proportion of susceptible individuals are fully vaccinated). The consequence of this result is that vaccination models for SARS-CoV-2 that do not explicitly account for age heterogeneity may be overestimating the level of vaccine-derived herd immunity threshold needed to eliminate the SARS-CoV-2 pandemic.

Implementation and adherence to regular asymptomatic testing in a COVID-19 vaccine trial

BACKGROUND

For pathogens which cause infections that present asymptomatically, evaluating vaccine efficacy (VE) against asymptomatic infection is important for understanding a vaccine's potential epidemiological impact. Regular testing for subclinical infections is a potentially valuable strategy but its success hinges on participant adherence and minimising false positives. This paper describes the implementation and adherence to weekly testing in a COVID-19 vaccine trial.

METHODS

COV002 was a phase 2/3 trial assessing the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2. Asymptomatic infections were detected using weekly self-administered swabs for RT-PCR testing. We analysed adherence using mixed-effects regression models and estimated the probability of true and false positive asymptomatic infections using estimates of adherence and testing characteristics.

FINDINGS

356,551 tests were self-administered by 10,811 participants during the 13-month follow-up. Median adherence was 75.0% (IQR 42·6-90·9), which translated to a 74·5% (IQR 50·9-78·8) probability of detecting a positive asymptomatic infection during the swabbing period, and between 21 and 96 false positives during VE evaluation. The odds of returning a swab declined by 8% per week and further after testing positive and unblinding. Adherence was higher in older age groups, females and non-healthcare workers.

INTERPRETATION

The COV002 trial demonstrated the feasibility of running a long-term regular asymptomatic testing strategy. This information could be valuable for designing future phase III vaccine trials in which infection is an outcome.

FUNDING

UK Research and Innovation, National Institutes for Health Research (NIHR), Coalition for Epidemic Preparedness Innovations, NIHR Oxford Biomedical Research Centre, Thames Valley and South Midland's NIHR Clinical Research Network, AstraZeneca.

A model-based assessment of social isolation practices for COVID-19 outbreak response in residential care facilities

BACKGROUND

Residential aged-care facilities (RACFs, also called long-term care facilities, aged care homes, or nursing homes) have elevated risks of respiratory infection outbreaks and associated disease burden. During the COVID-19 pandemic, social isolation policies were commonly used in these facilities to prevent and mitigate outbreaks. We refer specifically to general isolation policies that were intended to reduce contact between residents, without regard to confirmed infection status. Such policies are controversial because of their association with adverse mental and physical health indicators and there is a lack of modelling that assesses their effectiveness.

METHODS

In consultation with the Australian Government Department of Health and Aged Care, we developed an agent-based model of COVID-19 transmission in a structured population, intended to represent the salient characteristics of a residential care environment. Using our model, we generated stochastic ensembles of simulated outbreaks and compared summary statistics of outbreaks simulated under different mitigation conditions. Our study focuses on the marginal impact of general isolation (reducing social contact between residents), regardless of confirmed infection. For a realistic assessment, our model included other generic interventions consistent with the Australian Government's recommendations released during the COVID-19 pandemic: isolation of confirmed resident cases, furlough (mandatory paid leave) of staff members with confirmed infection, and deployment of personal protective equipment (PPE) after outbreak declaration.

RESULTS

In the absence of any asymptomatic screening, general isolation of residents to their rooms reduced median cumulative cases by approximately 27%. However, when conducted concurrently with asymptomatic screening and isolation of confirmed cases, general isolation reduced the median number of cumulative infections by only 12% in our simulations.

CONCLUSIONS

Under realistic sets of assumptions, our simulations showed that general isolation of residents did not provide substantial benefits beyond those achieved through screening, isolation of confirmed cases, and deployment of PPE. Our results also highlight the importance of effective case isolation, and indicate that asymptomatic screening of residents and staff may be warranted, especially if importation risk from the outside community is high. Our conclusions are sensitive to assumptions about the proportion of total contacts in a facility accounted for by casual interactions between residents.

High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark

Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding of SARS-CoV-2 emergence and spread. We examined the drivers of molecular evolution and spread of 291,791 SARS-CoV-2 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, and up to 80% of PCR-positive samples between March and November, the viral genome set is broadly whole-epidemic representative. We identify a consistent rise in viral diversity over time, with notable spikes upon the importation of novel variants (e.g., Delta and Omicron). By linking genomic data with rich individual-level demographic data from national registers, we find that individuals aged  < 15 and  > 75 years had a lower contribution to molecular change (i.e., branch lengths) compared to other age groups, but similar molecular evolutionary rates, suggesting a lower likelihood of introducing novel variants. Similarly, we find greater molecular change among vaccinated individuals, suggestive of immune evasion. We also observe evidence of transmission in rural areas to follow predictable diffusion processes. Conversely, urban areas are expectedly more complex due to their high mobility, emphasising the role of population structure in driving virus spread. Our analyses highlight the added value of integrating genomic data with detailed demographic and spatial information, particularly in the absence of structured infection surveys.

Asymptomatic infection and disappearance of clinical symptoms of COVID-19 infectors in China 2022-2023: a cross-sectional study

To explore the clinical characteristics of patients infected with SARS-CoV-2 nationwide, especially the effect factors of asymptomatic infection and disappearance of clinical symptoms. A total of 66,448 COVID-19 patients in China who have been diagnosed by nucleic acid test or rapid antigen test were surveyed online (December 24, 2022 to January 16, 2023). Our cross-sectional study used descriptive analyses and binary Logistics regression model to assess the correlation between the clinical characteristics and relative factors, including age, gender, pre-existing conditions, reinfection, vaccination and treatment. A total of 64,515 valid questionnaires were collected. Among included participants, 5969 of which were asymptomatic. The symptoms were mainly upper respiratory symptoms, including dry and itchy throat (64.16%), sore throat (59.95%), hoarseness (57.90%), nasal congestion (53.39%). In binary Logistics regression model, we found that male, no pre-existing conditions, reinfection and vaccination have positive correlations with the appearance of asymptomatic COVID-19 patients. In Cox proportional-hazards regression model, considering all clinical symptoms disappeared in 14 days as outcome, we found that ≤ 60 years old, male, no pre-existing conditions, vaccination and adopted treatment have positive correlations with rapid amelioration of clinical symptoms in COVID-19 patients. The clinical symptoms of the participants were mainly upper respiratory symptoms which were according with the infection of Omicron variant. Factors including age, gender, pre-existing conditions and reinfection could influence the clinical characteristics and prognosis of COVID-19 patients. Importantly, vaccination has positive significance for the prevention and treatment of COVID-19. Lastly, the use of Chinese medicine maybe beneficial to COVID-19 patients, however, reasonable guidance is necessary.

A proactive/reactive mass screening approach with uncertain symptomatic cases

We study the problem of mass screening of heterogeneous populations under limited testing budget. Mass screening is an essential tool that arises in various settings, e.g., the COVID-19 pandemic. The objective of mass screening is to classify the entire population as positive or negative for a disease as efficiently and accurately as possible. Under limited budget, testing facilities need to allocate a portion of the budget to target sub-populations (i.e., proactive screening) while reserving the remaining budget to screen for symptomatic cases (i.e., reactive screening). This paper addresses this decision problem by taking advantage of accessible population-level risk information to identify the optimal set of sub-populations for proactive/reactive screening. The framework also incorporates two widely used testing schemes: Individual and Dorfman group testing. By leveraging the special structure of the resulting bilinear optimization problem, we identify key structural properties, which in turn enable us to develop efficient solution schemes. Furthermore, we extend the model to accommodate customized testing schemes across different sub-populations and introduce a highly efficient heuristic solution algorithm for the generalized model. We conduct a comprehensive case study on COVID-19 in the US, utilizing geographically-based data. Numerical results demonstrate a significant improvement of up to 52% in total misclassifications compared to conventional screening strategies. In addition, our case study offers valuable managerial insights regarding the allocation of proactive/reactive measures and budget across diverse geographic regions.

Impact of COVID-19 and Non-COVID-19 Hospitalized Pneumonia on Longer-Term Cardiovascular Mortality in People With Type 2 Diabetes: A Nationwide Prospective Cohort Study From Scotland

OBJECTIVE

In this study we examine whether hospitalized coronavirus disease 2019 (COVID-19) pneumonia increases long-term cardiovascular mortality more than other hospitalized pneumonias in people with type 2 diabetes and aim to quantify the relative cardiovascular disease (CVD) mortality risks associated with COVID-19 versus non-COVID-19 pneumonia.

RESEARCH DESIGN AND METHODS

With use of the SCI-Diabetes register, two cohorts were identified: individuals with type 2 diabetes in 2016 and at the 2020 pandemic onset. Hospital and death records were linked for determination of pneumonia exposure and CVD deaths. Poisson regression estimated rate ratios (RRs) for CVD death associated with both pneumonia types, with adjustment for confounders. Median follow-up durations were 1,461 days (2016 cohort) and 700 days (2020 cohort).

RESULTS

The adjusted RR for CVD death following non-COVID-19 pneumonia was 5.51 (95% CI 5.31-5.71) prepandemic and 7.3 (6.86-7.76) during the pandemic. For COVID-19 pneumonia, the RR was 9.13 (8.55-9.75). Beyond 30 days post pneumonia, the RRs converged, to 4.24 (3.90-4.60) for non-COVID-19 and 3.35 (3.00-3.74) for COVID-19 pneumonia, consistent even with exclusion of prior CVD cases.

CONCLUSIONS

Hospitalized pneumonia, irrespective of causal agent, marks an increased risk for CVD death immediately and over the long-term. COVID-19 pneumonia poses a higher CVD death risk than other pneumonias in the short-term, but this distinction diminishes over time. These insights underscore the need for including pneumonia in CVD risk assessments, with particular attention to the acute impact of COVID-19 pneumonia.

SARS-CoV-2 dynamics in New York City during March 2020-August 2023

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widespread since 2020 and will likely continue to cause substantial recurring epidemics. However, understanding the underlying infection burden (i.e., including undetected asymptomatic/mild infections) and dynamics, particularly since late 2021 when the Omicron variant emerged, is challenging due to the potential for asymptomatic and repeat SARS-CoV-2 infection, changes in testing practices, and changes in disease reporting. Here, we leverage extensive surveillance data available in New York City (NYC) and a comprehensive model-inference system to reconstruct SARS-CoV-2 dynamics therein from the pandemic onset in March 2020 to August 2023, and further validate the estimates using independent wastewater surveillance data. The validated model-inference estimates indicate a very high infection burden totaling twice the population size (>5 times documented case count) but decreasing infection-fatality risk (a >10-fold reduction) during the first 3.5 years. The detailed estimates also reveal highly complex variant dynamics and immune landscape, changing virus transmissibility, and higher infection risk during winter in NYC over this time period. These transmission dynamics and drivers, albeit based on data in NYC, may be relevant to other populations and inform future planning to help mitigate the public health burden of SARS-CoV-2.

RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution

Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study utilized receptor-binding domain (RBD) amplicon sequencing of wastewater samples to monitor the SARS-CoV-2 community dynamics and evolution in El Paso, TX. Over 17 months, we identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Our findings demonstrated early detection of variants and identification of unreported outbreaks, while showing strong consistency with clinical genome sequencing data at the local, state, and national levels. Alpha diversity analyses revealed significant periodical variations, with the highest diversity observed in winter and the outbreak lag phases, likely due to lower competition among variants before the outbreak growth phase. The data underscores the importance of low transmission periods for rapid mutation and variant evolution. This study highlights the effectiveness of integrating RBD amplicon sequencing with wastewater surveillance in tracking viral evolution, understanding variant emergence, and enhancing public health preparedness.

Diagnostic Accuracy of the Abbott BinaxNOW COVID-19 Antigen Card Test, Puerto Rico

BACKGROUND

The COVID-19 pandemic underscored the need for rapid and accurate diagnostic tools. In August 2020, the Abbott BinaxNOW COVID-19 Antigen Card test became available as a timely and affordable alternative for SARS-CoV-2 molecular testing, but its performance may vary due to factors including timing and symptomatology. This study evaluates BinaxNOW diagnostic performance in diverse epidemiological contexts.

METHODS

Using RT-PCR as reference, we assessed performance of the BinaxNOW COVID-19 test for SARS-CoV-2 detection in anterior nasal swabs from participants of two studies in Puerto Rico from December 2020 to May 2023. Test performance was assessed by days post symptom onset, collection strategy, vaccination status, symptomatology, repeated testing, and RT-PCR cycle threshold (Ct) values.

RESULTS

BinaxNOW demonstrated an overall sensitivity of 84.1% and specificity of 98.8%. Sensitivity peaked within 1-6 days after symptom onset (93.2%) and was higher for symptomatic (86.3%) than asymptomatic (67.3%) participants. Sensitivity declined over the course of infection, dropping from 96.3% in the initial test to 48.4% in testing performed 7-14 days later. BinaxNOW showed 99.5% sensitivity in participants with low Ct values (≤ 25) but lower sensitivity (18.2%) for participants with higher Cts (36-40).

CONCLUSIONS

BinaxNOW demonstrated high sensitivity and specificity, particularly in early-stage infections and symptomatic participants. In situations where test sensitivity is crucial for clinical decision-making, nucleic acid amplification tests are preferred. These findings highlight the importance of considering clinical and epidemiological context when interpreting test results and emphasize the need for ongoing research to adapt testing strategies to emerging SARS-CoV-2 variants.

The effects of mouth rinsing and gargling with mouthwash containing povidone-iodine and hydrogen peroxide on the cycle threshold value of Severe Acute Respiratory Syndrome Coronavirus 2: A randomized controlled trial of asymptomatic and mildly symptomatic patients

Background

Coronavirus disease 2019 can spread rapidly. Surgery in the oral cavity poses a high risk of transmission of severe acute respiratory syndrome coronavirus 2. The American Dental Association and the Centers for Disease Control and Prevention recommend the use of mouthwash containing 1.5% hydrogen peroxide (H 2O 2) or 0.2% povidone iodine (PI) to reduce the viral load in the upper respiratory tract and decrease the risk of transmission. The aim of the present study was to analyze the effect of mouth rinsing and gargling with mouthwash containing 1% PI, 0.5% PI, 3% H 2O 2, or 1.5% H 2O 2 and water on the cycle threshold (CT) value obtained by real-time reverse transcription polymerase chain reaction (RT-PCR).

Methods

This study is a randomized single blind controlled clinical trial which has been registered in the International Standard Randomized Controlled Trial Number (ISRCTN) registry on the 3 rd February 2022 (Registration number: ISRCTN18356379). In total, 69 subjects recruited from Persahabatan General Hospital who met the inclusion criteria were randomly assigned to one of four treatment groups or the control group. The subjects were instructed to gargle with 15 mL of mouthwash for 30 s in the oral cavity followed by 30 s in the back of the throat, three times per day for 5 days. CT values were collected on postprocedural days 1, 3, and 5.

Results

The results of the Friedman test significantly differed among the groups (n=15). The CT values increased from baseline (day 0) to postprocedural days 1, 3, and 5.

Conclusions

Mouth rinsing and gargling with mouthwash containing 1% PI, 0.5% PI, 3% H 2O 2, or 1.5% H 2O 2 and water increased the CT value.